Hi Daniel,
I have used 6 vectors just for a trial run. This time I have used all the
260 vectors for the calculation ( Even though the protein have 293
residues, I have consider 260 vectors for calculation since I am
calculating the order parameters for CB-CG vector). I used 30,000 frames
for the calculation. Even though the calculation went successfully with
outputting order parameters for all 260 vectors, after the calculation I
got a message in the terminal that says " FYI: NEVEC > NELEM: Number of
calculated evecs were reduced to 260 ". What does this message means?
Thanks in advance
Regards
Anu
On Tue, Apr 9, 2013 at 8:28 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> On Tue, Apr 9, 2013 at 12:40 AM, anu chandra <anu80125.gmail.com> wrote:
> > Thanks for the reply. Now, as a trial run if I do with 6 vectors, I can
> > able to get the S2 order parameter, which seems to be reliable. Here is
> the
>
> Unless you have a specific reason for only using 6 vectors, I really
> do recommend that you define a vector for every N-H bond in your
> system for this calculation; the more information you have the more
> accurate the calculation will be.
>
> -Dan
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 201
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-9119 (Fax)
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Apr 09 2013 - 22:30:03 PDT
